Re: [outreach] Help trying to create R package

[Björn Höfling]

Hi Laura,

On Tue, 16 Oct 2018 22:01:58 -0300
Laura Lazzati <address@hidden> wrote:

> On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
> <address@hidden> wrote:
> >
> > Hi Laura,  
> Hi! I had not answered yet because I thought I would be too verbose.
> If so, please do a Laura -v instead of Laura -vvvvvvv.
> Thanks for writing :) it encourages me a lot.

You're welcome. It's nice to hear from your progress. Verbosity-level
is fine :-)

[..]

> > Here is another one:
> >
> > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt  
> 
> Something I faced after writing, was that in the link one of you
> provided: [1]https://guix.mdc-berlin.de/
> I have all the packages that are already available in guix. I like
> using the guix package command to practice that too, but i found it
> practical to see packages easier. I found out that package aspi
> (https://CRAN.R-project.org/package=aspi) is not available, and I
> would like to ask you if you believe it is a good candidate.
> One available package, according to [1] is r-abe
> (https://cran.r-project.org/web/packages/abe/index.html)

Sorry I have no clue of R at all. Could someone else please answer that
question, is r-aspi a good candidate?

https://cran.r-project.org/web/packages/aspi/index.html


> I wanted to see the template, so I ran:
> $ guix import cran abe
> And got the template, that matches even the version, and everything
> stated in the site.
> But then I tried:
> $ guix package -i r-abe and got no results.
> In fact, after running the command you have just provided, r-abe is
> not appearing in the r.txt file.
> I can't understand why that is happening. Am I missing something, or
> is there maybe an inconsistency between [1] and the guix installed in
> my foreign distro?

Concerning r-abe: I don't know how the list at guix-hpc is created
, how often it is updated or if there are extra packages in there. In
your case, I suppose you lack behind:

There is a commit for r-abe from 2019-09-13, so it is only a month old.
I think you are lacking behind. Have you done a `guix pull`? That's the
command used to update the package definitions.

In case you already did a guix pull recently, and you still don't see
it, there could be a problem with your $PATH, that the wrong guix is
coming first. Do a `which guix`.
Guix should be the one in ~/.config/guix/current/bin/guix


> Just wanted to install it to run guix edit to check if the suggested
> packages were already available or if I needed to package them too,
> but I have installed r-ade4, which has both imports and suggests, and
> I have just run:
> $guix import cran ade4
> And noticed that it only states in the template the Import package
> (MASS)

If I see that right, for R we only add the "Imports" packages, as they
are absolutely needed for compiling/running. All "Suggests" can be
installed/used just at runtime. Please correct me anyone if I'm wrong,
I'm not into R.

 
> Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> guix download from its site, and also guix hash to convert it to
> base32:
> 
> (define-public r-aspi
> (package
>   (name "r-aspi")
>   (version "0.2.0")
>   (source
>     (origin
>       (method url-fetch)
>       (uri (cran-uri "aspi" version))
>       (sha256
>         (base32
>           "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
>   (build-system r-build-system)
>    (home-page
>     "https://cran.r-project.org/web/packages/aspi/";)
>   (synopsis
>     "Analysis of Symmetry of Parasitic Infections")
>   (description
>     "Tools for the analysis and visualization of bilateral asymmetry
> in parasitic infections.")
>   (license gpl3+)))
> And that's were I ended up today (it is still Tuesday, almost 10pm)

I haven't done a full review, but that looks good. Next you need to get
the guix sources and prepare a patch.

That's described here:

https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing


Björn

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